Friday, August 31, 2012

I been watching proceedings at the Republican National Convention in Florida. If you think it's annoying for most liberal Americans, imagine what it's like for us furriners!

Coincidentally, we watched the last episode of The Newsroom a few days ago then decided to re-watch all ten episodes. It's one of the best shows on television. Makes me sad that The West Wing was cancelled. It's not a show that Republicans will enjoy.

Here's the clip from the first episode that sets the tone for a new kind of TV news show. The hero, Will McAvoy, is a cable news anchor who wants to tell it like it is instead of chasing ratings. The excerpt is from a town hall meeting at Northwestern University. A student has just asked why America is the greatest country in the world. (The student shows up again in Episode #10 when she wants to become a "greater fool.")

Not to be outdone, Ken Ham and the Creation Museum have taped a response ...

We are [responding to Nye] today with a video rebuttal featuring our “science guys” — Dr. David Menton and Dr. Georgia Purdom of our AiG and Creation Museum staff. These two PhD scientists were asked to reply to Mr. Nye, whose academic credentials do not come close to Drs. Menton and Purdom.

I present this for your amusement. I feel a bit sorry for Georgia Purdom since there's a high probability that some of her grandchildren are going to reject creationism. I wonder how she'll deal with that?

Actually it's not as bizarre as you might think. Lot's of people don't understand the ideas that Dawkins was pushing. He was mostly pointing out that evolution is a phenomenon that takes places at the level of genes and populations. Dawkins tweets that Rafford "gets it" in his review.

Thursday, August 30, 2012

Jerry Coyne and I have been thinking along the same lines. We've been reading a lot of books by philosophers and reading their articles and blogs. We're exploring the idea that philosophy and science are different ways of knowing, as the philosophers want us to believe. We've taken to heart the criticism from our philosopher friends that scientists have to understand more about philosophy.

Jerry and I (and many others) have reached the tentative conclusion that much of what passes for modern philosophy is a house of cards. It doesn't tell us anything. It doesn't produce knowledge, or truth.

Wednesday, August 29, 2012

A few years ago my university (University of Toronto) decided to take a look at student evaluations. A committee was formed and this was its terms of reference.

In recognition of the need to periodically revisit practices related to the evaluation of teaching, the Course Evaluation Working Group was formed in the Fall 2009 (Appendix B) and was asked to:

Review current course evaluation practices across the University of Toronto and at peer institutions;

Review current research on course evaluation policies and practices;

If necessary, make recommendations to improve existing policies and practices.

This sounds like a good idea. As you know, I am very skeptical about student evaluations [On the Significance of Student Evaluations]. It's abut time that universities took a long hard look at the process with a view to abolishing student evaluations or drastically revising them and reviewing their importance in promotion and tenure decisions. It's even more important to revise the policy on using student evaluations to judge the effectiveness of part-time lecturers and teaching assistants. At the very least, their role in determining teaching awards should be critically examined.

If I were in charge of this project I would pick a committee composed almost entirely of the following groups:

There would have to be substantial representation from undergraduates since they feel strongly about the issue and any drastic changes would require their consent and cooperation.

I would avoid having any administrators on the committee since the purpose of the committee was to evaluate existing university policy. In general, administrators are reluctant to make radical changes and they have trouble thinking outside the box. Furthermore, most of them don't have time to think seriously about the issue.

No students. No teaching assistants. No part-time lecturers. Very few people who are currently teaching large undergraduate courses. Almost every person has an administrative positions of some sort—most of the positions take up a considerable portion of their time and some of them are full-time jobs.

That's what thinking like an administrator looks like.

I don't think my university is unusual. We have thousands of very smart students and teachers but all the important committees seem to be composed of people with heavy administrative responsibilities. Does anyone understand the logic here?

Tuesday, August 28, 2012

Maybe it's just my imagination, but I think I detect a change on Evolution News & View and on Uncommon Descent. For years these blogs have been attacking evolution without paying the least attention to what their opponents are saying. Lately, however, there seem to be some authors who are actually listening to their opponents and trying to address the main criticisms of the IDiot position.

Sometimes you even see articles that are close to being scientifically correct and I've even seen articles that recognize the existence of modern evolutionary theory (i.e. not Darwinism).

The good articles are still quite rare but I'm encouraged by the fact that they are listening.

The latest contribution is by Stephen A. Batzer, a contributor to Evolution News & Views since May 10, 2012. Batzer has a Ph.D. in Mechanical Engineering (see The Salem Conjecture). He's responding to an earlier post of mine where I attempted to explain to Casey Luskin why he was wrong about evolutionary theory [Is "Unguided" Part of Modern Evolutionary Theory?]. Recall that Luskin was saying that the "unguided" nature of evolution was a core part of the theory of Darwinian evolution.

The Flying Spaghetti Monster is all-powerful and all-knowing and she loves meatballs. She is also very sneaky and doesn't want to leave any evidence of her existence. That's why she's very careful to only steal meatballs that won't be missed. (How often do you count the meatballs in your spaghetti?).

As far as I know this is a perfectly valid philosophical argument. If you accept the premises then it's quite possible that meatballs are disappearing from kitchens and restaurants without us ever being aware of the problem.

I'm not a philosopher but I strongly suspect that there aren't any papers on the possible existence of the Flying Spaghetti Monster in the philosophical literature. I doubt that there are any Ph.D. theses on the topic.

Monday, August 27, 2012

Last week's molecule was a small protein machine that pumps protons across a membrane (ubiquinol:cytochrome c oxidoreductase) [Monday's Molecule #182]. The winner was Stephen Spiro. I think he's a student at the University of Toronto (UT) but it's a campus I haven't heard of in a place called "Dallas."

This week's molecule is a lot less complicated although it's rather strange looking. This molecule has a very specific use. Name the molecule—the common name will do—and describe its use.

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is raltitrexed, also known as Tomudex. It's an inhibitor of the enzyme thymidylate synthase, the enzyme responsible for converting dUMP to dTMP. The drug is effective as an anti-cancer agent since it prevents cell division by blocking DNA synthesis. The winner is Raul A. Félix de Sousa (again).

Lots of people are having their genomes sequenced or otherwise analyzed for specific alleles. Those people should get all the information that comes out of the analyses although, hopefully, it will be scientifically correct information and any medical relevance will be explained by experts.1

There's another group of people who submit their genomes for research purposes only and they usually sign consent forms indicating that their name will not be associated with the results. Under those circumstances, the researchers should never have access to the individual's name or any circumstances that are not relevant to the study.

One of the first cases came a decade ago, just as the new age of genetics was beginning. A young woman with a strong family history of breast and ovarian cancer enrolled in a study trying to find cancer genes that, when mutated, greatly increase the risk of breast cancer. But the woman, terrified by her family history, also intended to have her breasts removed prophylactically.

Her consent form said she would not be contacted by the researchers. Consent forms are typically written this way because the purpose of such studies is not to provide medical care but to gain new insights. The researchers are not the patients’ doctors.

But in this case, the researchers happened to know about the woman’s plan, and they also knew that their study indicated that she did not have her family’s breast cancer gene. They were horrified.

This is a rather simple case of the researchers violating a standard protocol. They should not have known the identity of the patient and they should not have known what she intended to do.

Most of the "ethical problems" in the article are of this type. They involve researchers who are supposed to be concentrating on research and not on the treatment of individual patients. Those researchers have no idea whether the patients already know which alleles they carry or whether they are already undergoing medical treatment. That's just as it should be. If a DNA donor doesn't want to be contacted then it's ethically wrong for the researchers to violate that contract no matter how justified they think they are being. Furthermore, it should be impossible for them to find out the name and address of the donor so the issue should never come up.

That case is ethically straightforward compared to others, because the researchers could make a difference to an immediate medical decision. On the other hand, how many risk-free research participants went ahead with prophylactic mastectomies because researchers didn't know about their plans?

I think the article will be a good one for prompting student discussions in my courses, and I'll likely assign it widely. But I think the central ethical problem discussed in the article is temporary.

What will students learn from discussing issues like these? What controls are in place to make sure that students are informed about all the ethical issues? Will they be told that standard scientific protocols were violated once the researchers knew what the patient intended to do?

1. "Experts" do NOT include employees of any for-profit company that took money for sequencing the genome.

There's an interview with Tomoko Ohta in the August 21, 2012 issue of Current Biology: Tomoko Ohta.

You should know who she is but in case you don't, here's part of the brief bio ...

In 1973, she presented her first major paper entitled ‘Slightly deleterious mutant substitutions in evolution’. This theory was an expansion of Kimura's ‘neutral theory’, which Ohta called the ‘nearly neutral theory’ of molecular evolution. Her theory emphasizes the importance of interaction of drift and weak selection, and hence the role of slightly deleterious mutations in molecular evolution. With the accumulation of genome data, some of the predictions of the nearly neutral theory have been verified. The theory also provides a mechanism for the evolution of complex systems. Her other subject is to clarify the mechanisms of evolution and variation of multigene families. She has received several honors, including the foreign membership of the National Academy of Sciences, USA and Person of Cultural Merit, Japan.

It's very important to understand the essence of Nearly Neutral Theory since it explains the relationship between fitness and population size. Everyone needs to understand that Ohta demonstrated how slightly deleterious alleles can be fixed in a population. Her work showed that an allele can become effectively neutral in small populations even though it may actually lower the fitness of an individual. It's a way of explaining the limits of natural selection and of extending the Neutral Theory of Kimura.

She describes what happened when she joined Kimura's group at Tokyo.

At that time, Kimura was thinking of combining the theory of stochastic population genetics, the field he had been working on, with biochemical data on the nature of the genetic material. He proposed his now famous ‘neutral theory of molecular evolution’ in 1968. The ‘neutral theory’ proposed that most evolutionary changes at the molecular level were caused by random genetic drift rather than by natural selection. Note that the neutral theory classifies new mutations as deleterious, neutral, and advantageous. Under this classification, the rate of mutant substitutions in evolution can be formulated by the stochastic theory of population genetics. Kimura's theory was simple and elegant, yet I was not quite satisfied with it, because I thought that natural selection was not as simple as the mutant classification the neutral theory indicated, and that there would be border-line mutations with very small effects between the classes. I thus went ahead and proposed the nearly neutral theory of molecular evolution in 1973. The theory was not simple, and much more complicated, but to me, more realistic, and I have been working on this problem ever since.

This has nothing to do with Darwinism even though it's a fundamental part of modern evolutionary theory. You can't have an intelligent discussion about genome evolution, adaptationism, molecular evolution, or junk DNA without a firm grasp of Nearly Neutral Theory.

Tuesday, August 21, 2012

I want to draw your attention to an article in the July/August 2012 issue of Biochemistry and Molecular Biology Education (BAMBED). The authors are Michael Klymkowski and Melanie Cooper and the title is "Now for the Hard Part: The Path to Curricular Design."

There is a growing acknowledgement that STEM education, at all levels, is not producing learners with a deep understanding of core disciplinary concepts [1]. A number of efforts in STEM education reform have focused on the development of ‘‘student-centered’’ active learning environments, which, while believed to be more effective, have yet to be widely adopted [2]. What has not been nearly as carefully considered, however, is the role of the curriculum itself as perhaps the most persistent obstacle to effective science education. It is now time to examine not only how we teach, but also what we teach and how it affects student learning.

This is an important point. Most of the science education reforms that are being proposed these days focus on style rather than substance.

In the long run, it really doesn't matter whether you are employing the very latest pedagogical techniques if what you are teaching is crap.

But we also need to recognize that there's a relationship between what we teach and how we teach it. If you want to teach scientific thinking—as opposed to memorizing pathways—then there may be superior ways to do it.

Recognizing how challenging it is to build scientific understanding requires that we recognize that scientific thinking, in and of itself, is by no means easy and is certainly not ‘‘natural.’’ We are programmed by survival based and eminently practical evolutionary processes to ‘‘think fast’’ [8]. In contrast, scientific thinking is slow, hard, and difficult to maintain. If students are not exposed to environments where they must practice and use the skills (both metacognitive and procedural) that they need to learn, they may fall back on fast, surface level answers, and fail to recognize what it is that they do not understand.

Scientific thinking (and critical thinking) have to be experienced and practiced. That means you have to make time for that in your course.

Here's a podcast on the origin of life. Check out the website to see who's talking [Origin Stories].

For some strange reason the show begins with Greek mythology. Then it moves on to real science. There are three origin of life scenarios ...

Darwin's warm little pond ... equivalent to primordial soup.

Panspermia ... which doesn't solve anything.

Hydrothermal vents ... which aren't explained

The moderator seems to think that primordial soup has problems and panspermia is a nonstarter but he doesn't explain the hydrothermal vent story and doesn't even mention Metabolism First.

The second half of the show features soundbites suggesting that the origin of complex organic molecules on Earth is a problem but they could form in interstellar space. But this is exactly the "problem" that Metabolism First tries to explain so it's puzzling that there was no advocate of this view on the show.

This is a complicated topic that is not compatible with the format of this show. How do you, dear readers, think it rates as science journalism? Is this a good way to get the general public interested in science?

The blurb on the website suggests that the series is highly rated by fellow journalists.

A show that explores the bigger questions. Winner of "Top New Artists" and "Most Licensed by Public Radio Remix" awards at PRX's 2011 Zeitfunk Awards.

The authors of the paper, including Templeton Prize winner Francisco J Ayala, claim that pseduogenes exhibit two puzzling properties: (a) similar processed pseudogenes occur in mouse and humans suggesting that they are conserved, and (b) many pseudogenes are transcribed.

Processed pseudogenes arise when mRNA transcripts are reverse transcribed and inserted back into the genome. They usually come from genes that are highly expressed in germ line cells. Such genes tend to be highly conserved in related species. Mammals are closely related on the scale that were talking about. It's not surprising that a few new pseudogenes in such lineages are very similar in sequence. They're still pseudogenes. The vast majority of known pseudogenes are evolving at a rate that approximates the rate of mutation indicating that they are not constrained by negative selection.

Many pseudogenes are derived from gene duplications followed by mutations in one of the copies that make them incapable of producing a functional product. There's no reason to suspect that the first of these debilitating mutations will prevent transcription; therefore, one expects that many pseudogenes will be transcribed.

Some pseudogenes have been co-opted to provide a different function. There aren't very many examples but that doesn't stop the IDiots from making the fantastic leap from 0.0001% to 100%. (Pseudogenes represent about 1% of the genome [What's in Your Genome? ] so even if we assume that every single pseudogene is not a pseudogene, it hardly makes a dint in the amount of junk DNA.)

I discussed all this when I reviewed Jonathan Well's book The Myth of Junk DNA. The relevant chapter is Chapter 5 [Junk & Jonathan: Part 8—Chapter 5]. That review was posted in May 2011. It seems clear that the lawyers on the IDiot websites haven't read it.

Here's what one of them says on Uncommon Descent.

Darwin’s followers considered junk DNA powerful evidence for their theory, which is really a philosophy (often a cult), and that they often expressed that view, often triumphantly. Others insist it is true anyway.

The problem they hope to suppress is that if lots of junk in our DNA is such powerful evidence for their theory, then little junk throws it into doubt. That is, if it is such a good theory, why was it wrong on a point that was announced so triumphantly?

So it is a good thing that the science-minded public is reminded of the historical fact that Darwinism was supported by junk DNA. And it will be fun when the squirming editorials come out in science mags, warning people not to read too much into this, Darwin is still right.

I'm not even going to bother pointing out how stupid that is. If you're reading Sandwalk, chances are high that you could detect the lies1 with your eyes closed.

This week's molecule is one of the most important enzymes in the known universe. What is it?

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is complex III or ubiquinol:cytochrome c oxidoreductase, the enzyme responsible for the Q-cycle and the transport of proton across the plasma membrane of bacteria and the inner mitochondrial membrane in eukaryotes. This week's winner is Stephen Spiro.

This year's special issue of Scientific American is "Beyond the Limits of Science." One of the articles is about human evolution. The title is Super Humanity in the print issue but the online title is Aspiration Makes Us Human.

The author is Robert M. Sapolsky, a professor of biology and neurology at Stanford University in California (USA). Stanford is a pretty good school so he probably knows his stuff.

Here's how Sapolsky starts off ...

Sit down with an anthropologist to talk about the nature of humans, and you are likely to hear this chestnut: “Well, you have to remember that 99 percent of human history was spent on the open savanna in small hunter-gatherer bands.” It's a classic cliché of science, and it's true. Indeed, those millions of ancestral years produced many of our hallmark traits—upright walking and big brains, for instance.

This doesn't make sense.

Let's assume that our ancestors left Africa only 50,000 years ago. If that represents 1% of our evolutionary history then it means that our species and it's immediate direct ancestors lived on the African open savannah for 4,950,000 years.

Could that possibly be true even if you only count the main line of descent? What is the evidence that supports these claims? How much of the early history of Homo sapiens was influenced by adaptation to open savannah? Does anyone have a scientific answer to this question?

Setting aside the "main line," we now have good evidence that modern Homo sapiens acquired alleles from Neanderthals, Denisovans, and, perhaps more ancient Homo erectus. All three spent substantial time evolving in places that looked nothing like the open savannah in Africa. The proportion of the "invading" alleles may be only 10% or less but that's still significant.

Do we know for sure that all of the important features of modern humans came from alleles that were fixed by adaptation on the savannah? What if some of the more important behavioral alleles came from Neanderthals and became fixed because they were so much fitter than the savannah alleles?

Take the alleles that make women like to shop, for example. Maybe they arose in the Denisovans because they have access to better trade routes in central China? Maybe the women on the savannah preferred to store their cash in elephant tusks?

The evolutionary psychologists have developed awesome explanations for human behavior based on their detailed understanding of the social structure of hunter-gatherer groups living on the savannah for millions of years. What if our genetic ancestors lived elsewhere? The bad news is that all those just-so stories will be wrong. The good news is that they can publish a completely different set of stories and get twice as many publications.

Watch the video. Hemant makes the point that large churches in the USA provide a number of social services that, apparently, aren't available anywhere else. He points out that asking someone to give up their religion is asking them to give up all kinds of other things like volunteer groups, daycare, and support groups. Hemant thinks that atheists need to create "churches" that will fill these needs.

I don't get it. Why should atheists have to form their own "churches"? In Canada these services are provided by local community centres—there are four within a short drive of were I live. The one within walking distance is called South Common Community Centre. It has a swimming pool (see photo above), a public library, many gyms and exercise rooms, and meeting rooms. There's daycare and classes of various sorts, dozens of volunteer organizations and support groups, swimming lessons for adults and children and lots more. The community centres are funded by civic government and paid for by taxes. They are open to everybody.

Some of them rent out space for church services on Sundays but they are definitely secular. They are not atheist centres.

The best way to provide the services that people need has already been invented. It's called socialism. It's wrong to assume that the only solution is competing services supplied by various religious churches plus one non-religious church.

Is it impossible to work in America toward the goal of secular social services for all? Is that why the only solution seems to be for atheists/humanists to form their own competing religion to provide those services for nonbelievers?

Elsewhere on the internet there's a discussion about whether evolution can be disproved by simply finding a fossil out of order.

Here's what I said on Facebook ...

The statement is untrue. If we discover that a given species is older than we thought then we will just revise our view of the history of life on Earth. It will not disprove the fact of evolution and it will have no effect on evolutionary theory. It is a mistake to link the truth of evolution to our current understanding of the history of life. That history can be easily changed without threatening evolution.

It would have been nice to see the difference between pre-internet "bullies" and those on the internet. Are there any example of people who were "civilized" before they got on the internet but became bullies once they started a blog?

Wednesday, August 15, 2012

Nicholson was a professor of biochemistry at the University of Leeds in the United Kingdom. He started drawing metabolic charts back in 1955 and they gradually evolved into the works of art that you have seen in all the textbooks and on the walls of labs in offices in biochemistry departments around the world. I doubt that there's a single biochemist that hasn't studied these charts at some time during their undergraduate experience.

Lately his metabolic charts have been the property of the International Union of Biochemistry and Molecular Biology (IUBMB) but many of them have been marketed by Sigma-Aldrich [Metabolic Pathways].

Recent additions have included several minimaps of specific pathways such as those involved in lipid metabolism, glycolysis, the urea cycle etc. It's sad that we won't see any additions to this collection or any updates.

Modern atheists are often accused of being ignorant of the most up-to-date arguments for the existence of god(s).1 We are told that there's a very sophisticated group of theologians out there who shouldn't be ignored.

Whenever we ask for those "sophisticated" arguments for the existence of god(s) we are directed to various Courtier's Replies discussing how to rationalize the properties of various gods. They all begin with the assumption that god(s) exist. As I pointed out earlier, there's no reason why an atheist should care about things like the problem of evil. It makes about as much sense as debating the cut of the Emperor's new clothes or the stylishness of his new hat.

Alvin Plantinga is one of these "sophisticated" theologians. Listen to him explain why atheists should believe in god(s). Is this really the best they can do?

1. The second most common complaint is that we don't even have good arguments for atheism—at least not as good as those thinkers of the 20th century who were full of angst over not having a god to believe in. Apparently modern atheists aren't very sophisticated unless they are contemplating suicide.

Monday, August 13, 2012

Last week's molecule was an intermediate in some amino acid biosynthesis pathways and the enzyme that makes it is the target of Roundup®. Replacing this enzyme with a Roundup® resistant version yields genetically modified food plants [Monday's Molecule #180].

This week's molecule is a lot more complicated. You need to identify the specific type of molecule. Defective metabolism of this molecule is associated with a famous disease. Name the disease.

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is ganglioside GM2. Defects in ganglioside synthesis are responsible for a number of genetic diseases in humans including Tay-Sachs disease. This is the same molecule featured in Monday's Molecule #162 back on March 19, 2012. There was no winner that time.

This week's winner is Matt McFarlane, an undergraduate. He lives in Canada but he's quite far away and probably won't make it for lunch.

There's nothing in modern evolutionary theory that allows for mutations that arise specifically because they will produce a future benefit. That's why we say that mutations are "random" with respect to outcome.

There's nothing in the known history of life that suggests it has a purpose or direction. In particular, there's nothing to suggest that 3.5 billion years of evolution were just advanced preparation for the appearance of Home sapiens. That's why we say that evolution appears unguided and purposeless [Is "Unguided" Part of Modern Evolutionary Theory?]. And that's why anyone who says that life shows evidence of purpose is not being scientific.

Creationists aren't happy about this so they will go to extraordinary lengths to wiggle out of the inescapable conclusion based on solid evidence. The usual excuse is to postulate that god is very sneaky. He/she/it makes a huge effort to hide his/her/its manipulations so that it only appears that evolution is unguided and purposeless. The clever creationists aren't fooled by this sneaky god; they can detect its deception, but scientists can't.

Well, it's certainly true that many disciplines in the humanities are very unscientific—evolutionary psychology comes to mind—but this is one of the first times I've ever heard someone be proud of the fact that they don't think scientifically. Why in the world would she say that?

Turns out she's confused about what science is and what it isn't. She thinks that science requires lots of quantitative data and lots of mathematics and statistics.

Sometimes, there is no easy approach to studying the intricate vagaries that are the human mind and human behavior. Sometimes, we have to be okay with qualitative questions and approaches that, while reliable and valid and experimentally sound, do not lend themselves to an easy linear narrative—or a narrative that has a base in hard science or concrete math and statistics. Psychology is not a natural science. It’s a social science. And it shouldn’t try to be what it’s not.

Hmmmm ... that might explain a lot. I guess if you are seeking knowledge in the social sciences it's okay to use a non-scientific approach to gain knowledge. I wonder what approach they follow? Do they pray for guidance? Use a Ouija board? Or do they just make stuff up?

Maybe Konnikova is just saying that humanities disciplines are not chemistry, physics, biology or geology? Nah, that's too obvious. It doesn't merit an article in "Scientific" American. Maybe we'll find out what she really means when her book comes out in January. It's title is: Mastermind: How to Think Like Sherlock Holmes. Did Sherlock Holmes think like a scientist or did he think like someone in the humanities?

Chris Mulherin is an Anglican Minister who studies the relationship of science and religion. In this video he claims that science and religion are compatible. Specifically, science and Christianity are compatible.

He doesn't explain how rising from the dead, miracles, souls, heaven, and a Bible full of lies are compatible with science. Instead, he concentrates on the old saw of different magisteria. Christianity answers different questions than science and discovers different truths.

Id' like to echo the challenge I made some years ago and the one Jerry Coyne issues today [Do both science and faith produce truth?]. Can anyone give us an example of a "truth" discovered by religion—one that we all recognize as genuine knowledge? Name a "why" question that religion answers in a way that we all accept as meaningful and true.1

Those who think that science and religion are compatible like to accuse us of not understanding the serious philosophical issues. I don't think that's correct but, if it is, here's a chance for the serious courtier theologian to set us straight.

Waiting .....

1. It's not good enough to say that if only Christians accept the answer as true, then Christianity has discovered truth. If that were the case then astrology and homeopathy are also valid ways of finding truth even if astologers and homeopaths are the only ones who believe the answers. I'm guessing that no serious philosopher would defend such a ridiculous position.

An argument we are increasingly hearing from theistic evolutionists is that the "unguided" or "random" aspects of Darwinian evolution are merely "philosophical gloss" or an "add-on" promoted by new atheists who use bad philosophy. Jay Richards covered this question in his recent dialogue with Alvin Plantinga--see here, here, here, and here for the series. While many new atheists undoubtedly make poor philosophers, the "unguided" nature of Darwinian evolution is not a mere metaphysical "add on." Rather, it's a core part of how the theory of Darwinian evolution has been defined by its leading proponents. Unfortunately, even some eminent theistic and intelligent design-friendly philosophers appear unaware of the history and scientific development of neo-Darwinian theory.

This is wrong in many ways.

Here's the simple explanation ... so simple that even an IDiot should be able to understand it.

Modern evolutionary theory consists of many parts including the mechanisms of evolution. The main mechanisms are natural selection and random genetic drift and those two mechanisms act on populations containing variation. The variation is due to the presence of mutations and mutations arise "randomly" with respect to ultimate purpose or goal.

There are tons of experiments proving that mutations are essentially random. (Let's not get into quibbling about the meaning of "random.")

Now let's look at the history of life on Earth. This is a completely separate subject from evolutionary theory. It's like the difference between the theory of gravity and how and when our particular solar system formed.

Looking all the evidence used to reconstruct the probable history of life we see no evidence whatsoever that it was guided in any particular direction or that there was any underlying purpose. That's why we conclude that the evolution of life on Earth appears unguided. It's a tentative conclusion based on fact and observation and not on "the theory of Darwinian evolution."

While it is true that evolutionary theory doesn't allow for a "guided" mechanism, it isn't true that the history of life has to be devoid of purpose or guidance. There could well be evidence that god intervened or that particular organisms were preferred over others and the history was tilted in one direction. But there's no evidence that this is the case—with the possible exception of beetles.

The history of life looks exactly like it should if it were the result of accident, contingency, and evolution. There's no evidence of god(s). That's what makes the creationists upset, not evolutionary theory.

Friday, August 10, 2012

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.

This does not conform to my experience in the biological sciences.

I think that what usually what happens is that a new way of thinking is promoted by well-established investigators. Gradually other scientists are convinced by the evidence to change their minds and the new scientific truth spreads within the community.

When a substantial number of scientists are converted, they start teaching the new concept in graduate and undergraduate courses. This produces a young generation who never heard of the old "truth."

If I'm correct then a new generation of scientists grows up familiar with the new scientific truth but only because the established scientists converted and started training the next generation properly.

When it comes to challenging old established concepts in a discipline I find that initially the younger scientists are often quite conservative unless they just happen to be working on that problem. This shouldn't be a surprise since our young investigators have their hands full just establishing themselves in their field. They don't have time to think about what's going on in the rest of the discipline. In fact, it might be detrimental to their careers to challenge most established concepts.

As I'm writing this I'm having trouble coming up with examples in biology. Most of the conceptual shifts that come to mind are ongoing controversies where it still isn't clear that the new scientific truth will replace the old one. I'm thinking of evo-devo, challenges to evolutionary theory, junk DNA, chemiosmotic theory, metabolism & thermodynamics, the tree of life, photosynthesis, and even new ways of teaching.

Can anyone think of examples were the shift has been completed so we can test the Max Planck hypothesis?

How about the shift from thinking that genes were proteins to genes are DNA?

Believe it or not, the IDiots are still trying to weasel out of the mistakes they've made in attacking junk DNA.

Here's the problem. Jonathan Wells wrote an entire book on The Myth of Junk DNA. Wells says that back in the early 1970s a substantial number of scientists—he calls them Darwinists—said that all noncoding DNA was junk.

One of the things I'm interested in is the physical characteristics of planetary regoliths - the surface layer of broken rock, dust, etc., that covers planetary surfaces. It's important to understand how this layer formed and has evolved, because it holds a record of the geological processes that have occurred on each planet. Mars has a very complex surface geological record involving the actions of wind, volcanism, impact cratering, and possibly, water; so this new information about the composition and physical characteristics of the rocks at the Curiosity landing site will provide valuable new insights into the roles of these various processes in forming Mars' surface rocks.

For scientists, the best is yet to come. I hope the science journalists can keep the public focused on the real mission and the importance of the data.

Some of you aren't familiar with TED talks so the recent criticism doesn't make sense (e.g. The Trouble with TED). Here's an example of one of the problems with TED talks. This is a "gosh, gee whiz" kind of talk that's almost completely devoid of information.1

The talk has pretty pictures of the developing human embryo/fetus accompanied by the kind of music that evokes mystery and awe. The author of the video talks of the mystery and why it makes him think of divinity.

The first divinity-inspiring observation concerns collagen. Most collagen molecules form fibers (see Collagen) but those in the eye form sheets in the basal lamina. This is because the eye collagen is a different type of collagen. Here's what Wikipedia says [Collagen IV] ...

Type-IV collagen is a type of collagen found primarily in the basal lamina. The type IV collagen C4 domain at the C-terminus is not removed in post-translational processing, and the fibers link head-to-head, rather than in parallel. Also, type-IV lacks the regular glycine in every third residue necessary for the tight, collagen helix. This makes the overall arrangement more sloppy with kinks. These two features cause the collagen to form in a sheet, the form of the basal lamina.

Does that make you think of god(s)?

Would you pay several thousand dollars to hear this TED talk?

1. Recall that the theme of TED is "Ideas worth spreading." Which ideas in this talk are worth spreading?

While Miller and his fellow “soupists” blazed the initial paths in origins of life research, a startling new era dawned in the 80s with the discovery of potential life-sustaining factories in the most unlikely environments. The finding that life thrives in deep hydrothermal vents opened a whole new chapter in the field, again avowedly chemical. Black smoker chimneys located miles beneath the ocean have for millions of years been orchestrating a tumultuous union of hot, metal-rich, acidic chemicals arising from volcanic vents with cool alkaline waters. The unholy meeting of these two chemical opposites leads to a violent precipitation of minerals including the silicate mineral olivine, one of the most ubiquitous components of our planet’s rocky landscape. The precipitation of these minerals results in chimney like structures that can be miles high. The convecting thermal currents in these chimneys provide an abundant source of life’s sine qua non – energy. The metals can act as catalysts for simple reactions which involve sulfur, carbon monoxide and water. In recent years, because of the sheer energy hidden inside them, their capacity to catalyze key reactions like the Krebs cycle and concentrate reactants and products in microscopic pores and the uncanny resemblance of some of the iron and sulfur compounds to crucial iron-sulfur cores found in proteins, these mighty smokers have been considered by many scientists to precede or at least accompany the origin of life on the surface. Prominent among the “smokers” are scientists like Nick Lane and the patent attorney Günter Wächterhäuser who moonlights in the field as a “hobby”. These theories provide the “metabolism first” counterpart to the “replication first” camp. Together they may account for both genetic inheritance and chemical metabolism.

It doesn't matter whether you're a soupist or a smoker but you'd better be aware of the controversy. Too many scientists think that the primordial soup is still the best, and only, game in town in spite of its severe problems.

Some of you might recall the recent Chromosome 2 kerfuffle. It started when Carl Zimmer asked David Klinghoffer a simple question. Zimmer asked him to describe the evidence to support his claim that the fusion site didn't look like it should if two primitive ape chromosomes had fused to produce human chromosome 2.

Rather than simply answer the question, the IDiots circled the wagons then went into attack mode. Eventually, after a lot of pressure, they got around to answering the question; apparently there is no evidence to support their claim [And Finally the Hounding Duck Can Rest].

Of course by then they were so deep in their hole that the sun don't shine.

Last week we looked at an important intermediate in the Calvin cycle—the main pathway for fixing carbon dioxide in many species [Monday's Molecule #179]. Today we're going to look at the intermediate in another pathway. Name the molecule, the common name will do.

Discovery of this molecule, and the pathway it's involved in, was an important contribution to understanding basic metabolism in most cells. The enzyme that makes it has been characterized. It's now one of the most widely studied enzymes in biochemistry. The pathway is essential for all species, with a few minor exceptions.

This knowledge has been exploited by technology to an extent never imagined only 50 years ago. Name the technology and how it makes use of what we know about the enzyme and the pathway. For extra bonus points, explain how the molecule got it's root Japanese name.

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE:The molecule is 5-enolpyruvylshikimate 3-phosphate an intermediate in the chorismate pathway and the synthesis of tryptophan, phenylalanine, and tyrosine. The enzyme that produces this product is EPSP synthase and some bacterial versionsof this enzyme are resistant to glyphosate, the active ingredient in the herbicide Roundup®.

The gene for the resistant enzyme can be inserted into crop plants making them resistant to Roundup®.

The winner would have been Ben but I can't identify that person. The winner is Raul A. Félix de Sousa.

Blogging is fun. I love it when a serious discussion breaks out in the comments. Sometimes I love it even when the discussion is not serious.

Back in the olden days I used to love the newsgroups, especially talk.origins but I don't read it much any more. (Don't worry, I won't shut off the talk.origins server.)

Lately I've been spending more time on Twitter, Facebook and Google+ to see if there's anything there worth reading. It seems to be a mixed bag. The ratio of interesting vs non-interesting stuff seems to be a problem.

Monday, August 06, 2012

An awful of of people seem to waking up to the idea that TED talks are not what they're supposed to be. They attract a lot of kooks who can speak well and exude enthusiasm. How many times have you listened to a TED talk in your area of expertise and wondered how the heck that person got on the stage?

TED talks are just big soundbites and soundbites are not good ways to explain complicated, and potentially revolutionary, ideas.

The term "pH" is used to measure acidity. Strong acids, like hydrochloric acid or sulfuric acid, have very a very low pH while weaker acids, like acetic acid (vinegar), have pH readings that are higher. A "neutral pH" is 7.0, this is close to the pH value of the cytoplasm in living cells.

Higher pH values are "alkaline" rather that acidic. The highest pH value is usually shown as 14 and the lowest pH value is shown as 0.

Acidity is a function of the concentration of hydrogen ions (H+), or protons. The strength of alkaline solutions is measured by the concentration of hydroxide ions (OH-).

There's a reciprocal relationship between the concentrations of these two ions because we're dealing with aqueous solutions (water). Water molecules dissociate into H+ and OH- ions so in pure water there will always be equal concentrations of both ions.

The extent of this dissociation determines the concentration of these ions in pure water. We express the extent of dissociation using a term called the equilibrium constant (Keq) that is defined as the concentration of the products of a reaction over the concentration of the reactant(s).

Paul McBride is causing quite a stir among the creationists. His review of Science & Human Origins was so devastating that they couldn't ignore it.

Jonathan McLatchie (Jonathan M) is the latest creationist to attempt a defense of the home team. He concentrates on defending the Intelligent Design Creationist position on junk DNA [A Response to Paul McBride on Junk DNA].

On this topic (junk DNA), the IDiots make a lot of errors. One of them is to deliberately conflate "junk DNA" and "noncoding DNA" so that when they come up with evidence for function in noncoding DNA they can tout this as evidence against junk DNA. This error is so pervasive in the IDiot literature that Paul McBride even predicted that Casey Luskin would make this mistake in the book.

Today is the day that the Mars rover Curiosity landed. A remarkable American technological achievement. There have been many other technological achievements in the past century and it's wise to remember them

[reposted from August 6, 2009 (slightly modified)]

At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.

There are many arguments in favor of dropping the bomb, just as there are many arguments against it. What's clear is that in the context of 2012 we are not in a good position to judge the actions of countries that had been at war for many years.

The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that, you can really say that the victims of Hiroshima will have died in vain.

The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.

One of the many mistakes in Iraq was the naive assumption that it would be a clean war with few casualties and no long-term consequences for the Iraqi people. Yet today, the numbers of innocent lives lost in Iraq is comparable to the numbers lost in Hiroshima and Nagasaki. And what is the benefit for Iraq that outweighs the cost in human lives? Is it "freedom" and "democracy"?

Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of your foreign policy—it is an admission that you don't have a foreign policy.

[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.